Contacts of the helix formed by residues 19 - 33 (chain D) in PDB entry 4Q96


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with SER 19 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17D  SER*     3.2     7.0    +      -       -      -
     18D  ASN*     1.3    81.3    -      -       -      +
     20D  GLN*     1.3    64.5    +      -       -      +
     21D  HIS      3.5     1.0    +      -       -      -
     22D  SER*     2.9    17.5    +      -       -      -
     23D  VAL*     3.2    21.8    +      -       -      +
    208D  SO4      2.5    31.0    +      -       -      -
   1618F  THR*     6.3     1.1    -      -       -      -
   1619F  SER*     3.7    19.5    -      -       -      -
   1620F  PRO      3.6     7.0    -      -       -      -
   1621F  SER*     4.1     2.5    -      -       -      +
   1622F  TYR      3.7     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 20 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20B  GLN*     3.3    28.6    -      -       -      +
     19D  SER*     1.3    70.9    -      -       -      +
     21D  HIS*     1.3    62.3    +      -       -      +
     23D  VAL*     4.1     0.7    -      -       -      +
     24D  GLN*     2.7    56.3    +      -       -      +
     65D  ASP*     4.9     0.6    +      -       -      -
    204D  UNX      3.6    20.2    -      -       -      +
   1620F  PRO      2.8    19.1    +      -       -      +
   1621F  SER      4.2     2.5    -      -       -      +
   1622F  TYR*     3.2    23.6    -      -       -      +
   1623F  SER      3.0    27.5    +      -       -      -
   1626F  SER*     3.0    25.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 21 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  ARG*     3.8    40.8    +      -       -      +
     61B  TYR*     6.6     0.2    -      -       +      -
     19D  SER*     3.1     1.2    +      -       -      +
     20D  GLN*     1.3    80.4    -      -       -      +
     22D  SER*     1.3    59.3    +      -       -      +
     24D  GLN*     3.7    14.8    -      -       -      +
     25D  THR*     2.6    63.0    +      -       +      +
    204D  UNX      4.1     2.6    +      -       -      -
    208D  SO4      3.7    25.5    +      -       -      +
   1619F  SER*     4.3     5.1    +      -       -      +
   1620F  PRO      4.6     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 22 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15D  GLU      4.2     2.4    +      -       -      -
     16D  LEU*     3.4    12.3    -      -       -      +
     17D  SER*     2.9    49.6    +      -       -      -
     19D  SER*     2.9    11.3    +      -       -      -
     21D  HIS*     1.3    80.5    -      -       -      +
     23D  VAL*     1.3    62.9    +      -       -      +
     25D  THR*     3.8     3.2    -      -       -      -
     26D  LEU*     3.2    24.6    +      -       -      +
    208D  SO4      4.1     7.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 23 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16D  LEU*     3.9     9.4    -      -       +      -
     17D  SER      3.6    16.2    -      -       -      +
     18D  ASN      4.7     0.4    -      -       -      -
     19D  SER      3.2    13.7    +      -       -      +
     22D  SER*     1.3    77.4    -      -       -      +
     24D  GLN*     1.3    56.1    +      -       -      +
     27D  SER*     3.0    26.2    +      -       -      -
     58D  THR*     4.0    18.2    -      -       +      +
     61D  TYR*     4.0     2.0    -      -       +      +
     62D  LEU*     3.6    27.7    -      -       -      +
     65D  ASP*     4.1     4.7    -      -       +      -
   1622F  TYR*     3.6    50.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 24 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20B  GLN*     5.5     0.5    +      -       -      -
     20D  GLN*     2.7    63.0    +      -       -      +
     21D  HIS*     3.7    18.6    -      -       -      +
     23D  VAL*     1.3    78.1    -      -       -      +
     25D  THR*     1.3    61.8    +      -       -      +
     27D  SER*     3.6     7.2    -      -       -      -
     28D  LEU*     3.0    36.3    +      -       +      +
     65D  ASP*     4.2    12.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 25 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21D  HIS*     2.6    51.5    +      -       +      +
     22D  SER*     3.8     4.3    -      -       -      -
     24D  GLN*     1.3    77.9    -      -       -      +
     26D  LEU*     1.3    65.4    +      -       -      +
     28D  LEU*     3.3    12.3    +      -       +      +
     29D  TRP*     3.3    19.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 26 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9D  LEU*     4.5     3.6    -      -       +      -
     12D  LYS*     3.8    48.7    -      -       +      +
     13D  LEU*     3.8    17.3    -      -       +      -
     16D  LEU*     4.1    13.0    -      -       +      -
     22D  SER      3.2    14.9    +      -       -      +
     25D  THR*     1.3    76.8    -      -       -      +
     27D  SER*     1.3    65.2    +      -       -      +
     29D  TRP*     3.1     7.4    +      -       +      +
     30D  LEU*     3.0    42.7    +      -       +      +
     62D  LEU*     3.6    34.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 27 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23D  VAL      3.0    17.7    +      -       -      -
     24D  GLN      3.6     3.8    -      -       -      -
     25D  THR      3.3     0.2    -      -       -      -
     26D  LEU*     1.3    77.6    -      -       -      +
     28D  LEU*     1.3    56.5    +      -       -      +
     30D  LEU*     3.4     1.7    +      -       -      +
     31D  ILE*     3.0    37.4    +      -       -      +
     62D  LEU*     3.6     3.3    -      -       -      +
     65D  ASP*     2.7    37.4    +      -       -      -
     66D  VAL*     3.4    30.6    +      -       -      +
     69D  ASN*     4.4     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 28 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24D  GLN*     3.0    23.1    +      -       +      +
     25D  THR*     3.5    13.9    -      -       +      +
     27D  SER*     1.3    78.1    -      -       -      +
     29D  TRP*     1.3    57.1    +      -       -      +
     31D  ILE*     3.3    12.8    +      -       +      +
     32D  HIS*     2.9    28.5    +      -       -      +
     69D  ASN*     6.3     2.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 29 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4D  PHE*     3.8    43.1    -      +       -      -
      8D  ALA*     4.2    15.9    -      -       +      -
      9D  LEU*     4.6     9.6    -      -       -      -
     12D  LYS*     3.7    44.5    -      -       +      +
     25D  THR*     3.3     9.0    +      -       +      +
     26D  LEU*     3.1    14.1    +      -       +      +
     28D  LEU*     1.3    79.0    -      -       -      +
     30D  LEU*     1.3    81.3    +      -       +      +
     32D  HIS*     3.0    14.7    +      +       +      +
     33D  HIS*     2.9    59.9    +      +       -      -
----------------------------------------------------------
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Residues in contact with LEU 30 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4D  PHE*     5.1     0.2    -      -       +      -
      9D  LEU*     3.6    27.1    -      -       +      -
     26D  LEU*     3.0    21.5    +      -       +      +
     27D  SER      3.7     3.6    -      -       -      +
     29D  TRP*     1.3    90.0    -      -       +      +
     31D  ILE*     1.3    63.2    +      -       -      +
     33D  HIS*     3.1     6.1    +      -       -      +
     34D  ARG      3.1    17.5    +      -       -      -
     40D  ILE*     4.1    31.4    -      -       +      -
     44D  TRP*     6.1     1.1    -      -       +      -
     62D  LEU*     4.0    23.8    -      -       +      -
     66D  VAL*     3.9    25.1    -      -       +      -
     77D  PHE*     3.4    19.9    -      -       +      -
     81D  PHE*     6.4     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 31 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27D  SER*     3.0    29.8    +      -       -      +
     28D  LEU*     3.8    12.6    -      -       +      +
     30D  LEU*     1.3    72.4    -      -       -      +
     32D  HIS*     1.3    65.8    +      -       -      +
     34D  ARG*     3.2    29.8    +      -       -      +
     66D  VAL*     4.0    17.0    -      -       +      +
     69D  ASN*     3.4    35.7    -      -       +      +
     70D  SER*     3.6    18.8    -      -       -      +
     73D  LYS*     4.1    26.9    -      -       +      -
     77D  PHE*     4.2     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 32 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28D  LEU      2.9    14.3    +      -       -      +
     29D  TRP*     3.1    17.9    -      +       +      +
     31D  ILE*     1.3    79.5    -      -       -      +
     33D  HIS*     1.3    83.4    +      +       -      +
     34D  ARG*     3.3    11.6    +      -       -      +
     35D  LYS*     5.1     1.7    +      -       -      +
    209D  SO4      5.1     0.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 33 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4D  PHE*     3.5    21.1    +      -       +      +
     29D  TRP*     2.9    71.1    +      +       -      +
     30D  LEU*     3.1     7.8    +      -       -      +
     32D  HIS*     1.3    98.0    +      +       -      +
     34D  ARG*     1.3    56.4    +      -       -      +
     35D  LYS*     3.1     5.2    -      -       -      +
     36D  HIS*     3.0    29.2    +      -       +      -
     40D  ILE*     3.3    14.1    -      -       +      +
    209D  SO4      2.8    39.2    +      -       -      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il